Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.

ABSTRACT: Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.

SUBMITTER: Skoruppa E

PROVIDER: S-EPMC6132066 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.

Skoruppa Enrico E Nomidis Stefanos K SK Marko John F JF Carlon Enrico E

Physical review letters 20180801 8

Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows ...[more]

PMID: 30192578

Similar Datasets

Biaxiality-driven twist-bend to splay-bend nematic phase transition induced by an electric field.

Project description:Although the existence of the twist-bend (NTB) and splay-bend (NSB) nematic phases was predicted long ago, only the former has as yet been observed experimentally, whereas the latter remains elusive. This is especially disappointing because the NSB nematic is promising for applications in electro-optic devices. By applying an electric field to a planar cell filled with the compound CB7CB, we have found an NTB-NSB phase transition using birefringence measurements. This field-induced transition to the biaxial NSB occurred, although the field was applied along the symmetry axis of the macroscopically uniaxial NTB Therefore, this transition is a counterintuitive example of breaking of the macroscopic uniaxial symmetry. We show by theoretical modeling that the transition cannot be explained without considering explicitly the biaxiality of both phases at the microscopic scale. This strongly suggests that molecular biaxiality should be a key factor favoring the stability of the NSB phase.

| S-EPMC7467706 | biostudies-literature

Induced smectic phase in binary mixtures of twist-bend nematogens.

Project description:The investigation of liquid crystal (LC) mixtures is of great interest in tailoring material properties for specific applications. The recent discovery of the twist-bend nematic phase (NTB) has sparked great interest in the scientific community, not only from a fundamental viewpoint, but also due to its potential for innovative applications. Here we report on the unexpected phase behaviour of a binary mixture of twist-bend nematogens. A binary phase diagram for mixtures of imino-linked cyanobiphenyl (CBI) dimer and imino-linked benzoyloxy-benzylidene (BB) dimer shows two distinct domains. While mixtures containing less than 35 mol % of BB possess a wide temperature range twist-bend nematic phase, the mixtures containing 55-80 mol % of BB exhibit a smectic phase despite that both pure compounds display a Iso-N-NTB-Cr phase sequence. The phase diagram shows that the addition of BB of up to 30 mol % significantly extends the temperature range of the NTB phase, maintaining the temperature range of the nematic phase. The periodicity, obtained by atomic force microscopy (AFM) imaging, is in the range of 6-7 nm. The induction of the smectic phase in the mixtures containing 55-80 mol % of BB was confirmed using polarising optical microscopy (POM), differential scanning calorimetry (DSC) and X-ray diffraction. The origin of the intercalated smectic phase was unravelled by combined spectroscopic and computational methods and can be traced to conformational disorder of the terminal chains. These results show the importance of understanding the phase behaviour of binary mixtures, not only in targeting a wide temperature range but also in controlling the self-organizing processes.

| S-EPMC5942249 | biostudies-literature

A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA.

Project description:As superfamily 2 (SF2)-type translocases, chromatin remodelers are expected to use an inchworm-type mechanism to walk along DNA. Yet how they move DNA around the histone core has not been clear. Here we show that a remodeler ATPase motor can shift large segments of DNA by changing the twist and length of nucleosomal DNA at superhelix location 2 (SHL2). Using canonical and variant 601 nucleosomes, we find that the Saccharomyces cerevisiae Chd1 remodeler decreased DNA twist at SHL2 in nucleotide-free and ADP-bound states, and increased twist with transition state analogs. These differences in DNA twist allow the open state of the ATPase to pull in ~1 base pair (bp) by stabilizing a small DNA bulge, and closure of the ATPase to shift the DNA bulge toward the dyad. We propose that such formation and elimination of twist defects underlie the mechanism of nucleosome sliding by CHD-, ISWI-, and SWI/SNF-type remodelers.

| S-EPMC6031429 | biostudies-literature

The Dependency of Nematic and Twist-bend Mesophase Formation on Bend Angle.

Project description:We have prepared and studied a family of cyanobiphenyl dimers with varying linking groups with a view to exploring how molecular structure dictates the stability of the nematic and twist-bend nematic mesophases. Using molecular modelling and 1D 1H NOESY NMR spectroscopy, we determine the angle between the two aromatic core units for each dimer and find a strong dependency of the stability of both the nematic and twist-bend mesophases upon this angle, thereby satisfying earlier theoretical models.

| S-EPMC5098182 | biostudies-literature

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.

Project description:ATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler translocase in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the translocase overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of a pair of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these key biological processes.

| S-EPMC6237416 | biostudies-literature

Making the bend: DNA tertiary structure and protein-DNA interactions.

Project description:DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence ("base readout") as well as the intrinsic DNA structure ("shape recognition"). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics.

| S-EPMC4139847 | biostudies-literature

Origin of twist-bend coupling in actin filaments.

Project description:Actin filaments are semiflexible polymers that display large-scale conformational twisting and bending motions. Modulation of filament bending and twisting dynamics has been linked to regulatory actin-binding protein function, filament assembly and fragmentation, and overall cell motility. The relationship between actin filament bending and twisting dynamics has not been evaluated. The numerical and analytical experiments presented here reveal that actin filaments have a strong intrinsic twist-bend coupling that obligates the reciprocal interconversion of bending energy and twisting stress. We developed a mesoscopic model of actin filaments that captures key documented features, including the subunit dimensions, interaction energies, helicity, and geometrical constraints coming from the double-stranded structure. The filament bending and torsional rigidities predicted by the model are comparable to experimental values, demonstrating the capacity of the model to assess the mechanical properties of actin filaments, including the coupling between twisting and bending motions. The predicted actin filament twist-bend coupling is strong, with a persistence length of 0.15-0.4 ?m depending on the actin-bound nucleotide. Twist-bend coupling is an emergent property that introduces local asymmetry to actin filaments and contributes to their overall elasticity. Up to 60% of the filament subunit elastic free energy originates from twist-bend coupling, with the largest contributions resulting under relatively small deformations. A comparison of filaments with different architectures indicates that twist-bend coupling in actin filaments originates from their double protofilament and helical structure.

| S-EPMC2941021 | biostudies-other

Twist-Bend Nematic Phase from the Landau-de Gennes Perspective.

Project description:Generalized Landau-de Gennes theory is proposed that comprehensively explains currently available experimental data for the heliconical twist-bend nematic (NTB) phase observed in liquid crystalline systems of chemically achiral bent-core-like molecules. A bifurcation analysis gives insight into possible structures that the model can predict and guides in the numerical analysis of relative stability of the isotropic (I), uniaxial nematic (NU), and twist-bend nematic phases. An estimate of constitutive parameters of the model from temperature variation of the nematic order parameter and the Frank elastic constants in the nematic phase enables us to demonstrate quantitative agreement between the calculated and experimentally determined temperature dependence of the pitch and conical angle in NTB. Properties of order parameters also explain a puzzling lack of a half-pitch band in resonant soft X-ray scattering. Other key findings of the model are predictions of I-NTB and NU-NTB tricritical points and insight into biaxiality of NTB.

| S-EPMC7662770 | biostudies-literature

Nematic twist-bend phase with nanoscale modulation of molecular orientation.

Project description:A state of matter in which molecules show a long-range orientational order and no positional order is called a nematic liquid crystal. The best known and most widely used (for example, in modern displays) is the uniaxial nematic, with the rod-like molecules aligned along a single axis, called the director. When the molecules are chiral, the director twists in space, drawing a right-angle helicoid and remaining perpendicular to the helix axis; the structure is called a chiral nematic. Here using transmission electron and optical microscopy, we experimentally demonstrate a new nematic order, formed by achiral molecules, in which the director follows an oblique helicoid, maintaining a constant oblique angle with the helix axis and experiencing twist and bend. The oblique helicoids have a nanoscale pitch. The new twist-bend nematic represents a structural link between the uniaxial nematic (no tilt) and a chiral nematic (helicoids with right-angle tilt).

| S-EPMC3831290 | biostudies-other

A generalized density-modulated twist-splay-bend phase of banana-shaped particles.

Project description:In 1976, Meyer predicted that bend distortions of the nematic director field are complemented by deformations of either twist or splay, yielding twist-bend and splay-bend nematic phases, respectively. Four decades later, the existence of the splay-bend nematic phase remains dubious, and the origin of these spontaneous distortions uncertain. Here, we conjecture that bend deformations of the nematic director can be complemented by simultaneous distortions of both twist and splay, yielding a twist-splay-bend nematic phase. Using theory and simulations, we show that the coupling between polar order and bend deformations drives the formation of modulated phases in systems of curved rods. We find that twist-bend phases transition to splay-bend phases via intermediate twist-splay-bend phases, and that splay distortions are always accompanied by periodic density modulations due to the coupling of the particle curvature with the non-uniform curvature of the splayed director field, implying that the twist-splay-bend and splay-bend phases of banana-shaped particles are actually smectic phases.

| S-EPMC8041804 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data